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- PDB-5aa7: Structural and functional characterization of a chitin-active 15.... -

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Basic information

Entry
Database: PDB / ID: 5aa7
TitleStructural and functional characterization of a chitin-active 15.5 kDa lytic polysaccharide monooxygenase domain from a modular chitinase from Jonesia denitrificans
ComponentsCHITINASE
KeywordsHYDROLASE
Function / homology
Function and homology information


chitinase / chitinase activity / chitin catabolic process / chitin binding / carbohydrate binding / carbohydrate metabolic process / extracellular region / metal ion binding
Similarity search - Function
chitin-binding protein cbp21 / Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / Carbohydrate-binding module family 5/12 / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Coagulation Factor XIII; Chain A, domain 1 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. ...chitin-binding protein cbp21 / Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / Carbohydrate-binding module family 5/12 / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Coagulation Factor XIII; Chain A, domain 1 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Distorted Sandwich / Immunoglobulin E-set / Glycoside hydrolase superfamily / Mainly Beta
Similarity search - Domain/homology
COPPER (I) ION / Chitinase
Similarity search - Component
Biological speciesJONESIA DENITRIFICANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsMekasha, S. / Forsberg, Z. / Dalhus, B. / Choudhary, S. / Schmidt-Dannert, C. / Vaaje-Kolstad, G. / Eijsink, V.
CitationJournal: FEBS Lett. / Year: 2016
Title: Structural and Functional Characterization of a Small Chitin-Active Lytic Polysaccharide Monooxygenase Domain of a Multi-Modular Chitinase from Jonesia Denitrificans.
Authors: Mekasha, S. / Forsberg, Z. / Dalhus, B. / Bacik, J. / Choudhary, S. / Schmidt-Dannert, C. / Vaaje-Kolstad, G. / Eijsink, V.G.H.
History
DepositionJul 23, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Apr 6, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHITINASE
B: CHITINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2134
Polymers31,0862
Non-polymers1272
Water5,909328
1
A: CHITINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6062
Polymers15,5431
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CHITINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6062
Polymers15,5431
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.760, 74.330, 119.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CHITINASE / 3LPMOA


Mass: 15542.896 Da / Num. of mol.: 2
Fragment: 15.5 KDA LYTIC POLYSACCHARIDE MONOOXYGENASE, RESIDUES 32-17 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) JONESIA DENITRIFICANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: C7R4I0, chitinase
#2: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.66 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.37778
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.37778 Å / Relative weight: 1
ReflectionResolution: 1.5→46.51 Å / Num. obs: 45097 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 11.3 Å2 / Rsym value: 0.05 / Net I/σ(I): 30.3
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 5.4 / Rsym value: 0.25 / % possible all: 79.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
SHELXEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.55→37.165 Å / SU ML: 0.09 / σ(F): 0 / Phase error: 14.42 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1743 2033 4.9 %
Rwork0.1498 --
obs0.151 41687 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→37.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2188 0 2 328 2518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062323
X-RAY DIFFRACTIONf_angle_d1.0743207
X-RAY DIFFRACTIONf_dihedral_angle_d12.613823
X-RAY DIFFRACTIONf_chiral_restr0.073358
X-RAY DIFFRACTIONf_plane_restr0.005428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.58610.16581070.15322460X-RAY DIFFRACTION92
1.5861-1.62570.17791360.14762520X-RAY DIFFRACTION98
1.6257-1.66970.17731290.14552635X-RAY DIFFRACTION100
1.6697-1.71880.16311340.14422603X-RAY DIFFRACTION100
1.7188-1.77430.19631450.15032631X-RAY DIFFRACTION100
1.7743-1.83770.18631380.1532606X-RAY DIFFRACTION100
1.8377-1.91130.17491240.14552625X-RAY DIFFRACTION100
1.9113-1.99830.14361580.14892632X-RAY DIFFRACTION100
1.9983-2.10360.16121280.1462648X-RAY DIFFRACTION100
2.1036-2.23540.17011380.14652646X-RAY DIFFRACTION100
2.2354-2.4080.17471500.1582647X-RAY DIFFRACTION100
2.408-2.65020.21031340.16932709X-RAY DIFFRACTION100
2.6502-3.03360.21561360.1662657X-RAY DIFFRACTION100
3.0336-3.82130.16841380.13892740X-RAY DIFFRACTION100
3.8213-37.17570.1451380.14042895X-RAY DIFFRACTION100

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